Diffusion model methods are frequently applied in monitoring water-atmosphere methane (CH4) fluxes. To explore the variation character and influence factors of CH4 transfer velocity (kx) and diffusive fluxes across the water-atmosphere interface from aquaculture shrimp ponds, this study chooses six different model methods for estimating kx and CH4 diffusive fluxes in the Min River estuary (MRE) and Jiulong River estuary (JRE) on the southeast coast of China. For each estuary, water samples were collected using a hydrophore sampler from three shrimp ponds in June, August, and October 2015, respectively. Meanwhile, meteorological parameter (air temperature, wind speed and atmospheric pressure) and water-quality indicators (water temperature, pH, dissolved oxygen and salinity) were measured in situ using a portable instrument. A headspace equilibration technique was used for the measurement of dissolved CH4 concentration. The mean kx at MRE and JRE ponds during the study period ranged between 1.60±0.75 and 6.29±1.30 cm/h, and 0.89±0.19 and 6.07±0.61 cm/h,respectively. The mean CH4 diffusive fluxes in the MRE and JRE ponds over the study period ranged between 9.19±2.67 and 30.64±6.28 μmol/(m2·h), and 3.18±0.48 and 21.03±2.13 μmol/(m2·h), respectively. The results showed that kx and CH4 diffusive fluxes across the water-atmosphere interface from the estuaries of shrimp ponds greatly varied in spatial and seasonal dynamics. The CH4 diffusive fluxes were significantly higher from the shrimp ponds in the Min River estuary than in the Jiulong River estuary (P<0.05). Average seasonal kx (or CH4 diffusive fluxes) in MRE and JRE shows an increasing trend over time. The wind speed, water dissolved CH4 concentration and salinity are important factors that drive the changes in CH4 diffusive fluxes emission. There are differences in CH4 transfer velocity across the water-atmosphere interface from aquaculture shrimp ponds between the different model methods, indicating that the CH4 diffusive fluxes from the model-based estimation has a certain degree of uncertainty.